Created User Manual

README.md

@@ -6,6 +6,8 @@ PDBFixer is an easy to use application for fixing problems in Protein Data Bank
 - Add missing heavy atoms.
 - Add missing heavy atoms.
 - Add missing hydrogen atoms.
 - Add missing hydrogen atoms.
 - Build missing loops.
 - Build missing loops.
-- Convert non-standard amino acids to their standard equivalents.
+- Convert non-standard residues to their standard equivalents.
 - Select a single position for atoms with multiple alternate positions listed.
 - Select a single position for atoms with multiple alternate positions listed.
-- Delete unwanted chains from the model.
+- Delete unwanted chains from the model.
\ No newline at end of file
+- Delete unwanted heterogens.
+- Build a water box for explicit solvent simulations.
\ No newline at end of file

pdbfixer.py

@@ -386,7 +386,7 @@ class PDBFixer(object):
     def findMissingAtoms(self):
     def findMissingAtoms(self):
         """Find heavy atoms that are missing from the structure.
         """Find heavy atoms that are missing from the structure.
         
         
-        The results are stored into two field: missingAtoms and missingTerminals.  Each of these is a dict whose keys
+        The results are stored into two fields: missingAtoms and missingTerminals.  Each of these is a dict whose keys
         are Residue objects and whose values are lists of atom names.  missingAtoms contains standard atoms that should
         are Residue objects and whose values are lists of atom names.  missingAtoms contains standard atoms that should
         be present in any residue of that type.  missingTerminals contains terminal atoms that should be present at the
         be present in any residue of that type.  missingTerminals contains terminal atoms that should be present at the
         start or end of a chain.
         start or end of a chain.
@@ -645,7 +645,7 @@ if __name__=='__main__':
         parser.add_option('--water-box', dest='box', type='float', nargs=3, metavar='X Y Z', help='add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]')
         parser.add_option('--water-box', dest='box', type='float', nargs=3, metavar='X Y Z', help='add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]')
         parser.add_option('--ph', type='float', default=7.0, dest='ph', help='the pH to use for adding missing hydrogens [default: 7.0]')
         parser.add_option('--ph', type='float', default=7.0, dest='ph', help='the pH to use for adding missing hydrogens [default: 7.0]')
         parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
         parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
-        parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='positive ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
+        parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
         parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')
         parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')
         (options, args) = parser.parse_args()
         (options, args) = parser.parse_args()
         if len(args) == 0:
         if len(args) == 0: